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3MV6
Asym. Unit
Info
Asym.Unit (237 KB)
Biol.Unit 1 (911 KB)
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(1)
Title
:
AXIAL LIGAND SWAPPING IN DOUBLE MUTANT MAINTAINS INTRADIOL-CLEAVAGE CHEMISTRY IN PROTOCATECHUATE 3,4-DIOXYGENASE
Authors
:
V. M. Purpero, J. D. Lipscomb
Date
:
03 May 10 (Deposition) - 01 Jun 11 (Release) - 01 Jun 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.86
Chains
:
Asym. Unit : A,B,C,M,N,O
Biol. Unit 1: A,B,C,M,N,O (4x)
Keywords
:
Intradiol, Dioxygenase, Es Complex, , Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
V. M. Purpero, J. D. Lipscomb
Axial Ligand Swapping In Double Mutant Maintains Intradiol-Cleavage Chemistry In Protocatechuate 3, 4-Dioxygenase
To Be Published
[
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Hetero Components
(6, 23)
Info
All Hetero Components
1a: BETA-MERCAPTOETHANOL (BMEa)
1b: BETA-MERCAPTOETHANOL (BMEb)
1c: BETA-MERCAPTOETHANOL (BMEc)
1d: BETA-MERCAPTOETHANOL (BMEd)
1e: BETA-MERCAPTOETHANOL (BMEe)
1f: BETA-MERCAPTOETHANOL (BMEf)
2a: CHLORIDE ION (CLa)
3a: 3,4-DIHYDROXYBENZOIC ACID (DHBa)
3b: 3,4-DIHYDROXYBENZOIC ACID (DHBb)
3c: 3,4-DIHYDROXYBENZOIC ACID (DHBc)
4a: FE (III) ION (FEa)
4b: FE (III) ION (FEb)
4c: FE (III) ION (FEc)
5a: GLYCEROL (GOLa)
5b: GLYCEROL (GOLb)
5c: GLYCEROL (GOLc)
6a: SULFATE ION (SO4a)
6b: SULFATE ION (SO4b)
6c: SULFATE ION (SO4c)
6d: SULFATE ION (SO4d)
6e: SULFATE ION (SO4e)
6f: SULFATE ION (SO4f)
6g: SULFATE ION (SO4g)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BME
6
Ligand/Ion
BETA-MERCAPTOETHANOL
2
CL
1
Ligand/Ion
CHLORIDE ION
3
DHB
3
Ligand/Ion
3,4-DIHYDROXYBENZOIC ACID
4
FE
3
Ligand/Ion
FE (III) ION
5
GOL
3
Ligand/Ion
GLYCEROL
6
SO4
7
Ligand/Ion
SULFATE ION
[
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Sites
(23, 23)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASN A:37 , THR A:105 , HIS A:107
BINDING SITE FOR RESIDUE SO4 A 201
02
AC2
SOFTWARE
HIS A:48 , LYS A:180
BINDING SITE FOR RESIDUE SO4 A 202
03
AC3
SOFTWARE
THR A:169 , ILE A:171 , ARG A:184 , PHE A:185 , ASP A:186 , ARG A:188
BINDING SITE FOR RESIDUE GOL A 203
04
AC4
SOFTWARE
ASN B:37 , ARG B:38 , THR B:105 , HIS B:107 , HOH B:618
BINDING SITE FOR RESIDUE SO4 B 201
05
AC5
SOFTWARE
HIS B:61 , LEU B:62 , ARG B:64 , HOH B:672 , GLN C:163 , GLN C:165
BINDING SITE FOR RESIDUE SO4 B 202
06
AC6
SOFTWARE
ILE B:171 , ARG B:184 , PHE B:185 , ASP B:186 , ARG B:188
BINDING SITE FOR RESIDUE BME B 203
07
AC7
SOFTWARE
GLU B:34 , ILE B:35 , TRP B:36 , ASN B:37 , ARG B:38 , TYR B:83 , LEU B:85 , HOH B:230 , HOH B:297
BINDING SITE FOR RESIDUE BME B 204
08
AC8
SOFTWARE
ASN C:37 , THR C:105 , HIS C:107
BINDING SITE FOR RESIDUE SO4 C 201
09
AC9
SOFTWARE
ILE C:171 , ARG C:184 , PHE C:185 , ASP C:186 , ARG C:188
BINDING SITE FOR RESIDUE GOL C 202
10
BC1
SOFTWARE
ARG C:38 , LEU C:39 , ASN C:84 , LEU C:85 , ASN C:87 , ASN C:90
BINDING SITE FOR RESIDUE GOL C 203
11
BC2
SOFTWARE
ARG M:409 , PRO M:421
BINDING SITE FOR RESIDUE BME M 1
12
BC3
SOFTWARE
TYR M:408 , HIS M:460 , TYR M:462 , DHB M:539
BINDING SITE FOR RESIDUE FE M 600
13
BC4
SOFTWARE
PRO A:15 , TYR A:16 , HOH A:374 , HOH M:137 , TYR M:408 , HIS M:447 , TRP M:449 , ARG M:457 , HIS M:460 , TYR M:462 , HOH M:540 , FE M:600 , HOH M:884
BINDING SITE FOR RESIDUE DHB M 539
14
BC5
SOFTWARE
ARG N:414 , ARG N:450
BINDING SITE FOR RESIDUE SO4 N 6
15
BC6
SOFTWARE
ARG N:333
BINDING SITE FOR RESIDUE BME N 1
16
BC7
SOFTWARE
THR N:321 , PRO N:322 , ASP N:323 , LYS N:493 , HOH N:752
BINDING SITE FOR RESIDUE BME N 539
17
BC8
SOFTWARE
GLY N:357 , ALA N:358 , HIS N:359 , ASP N:360 , ASN N:366
BINDING SITE FOR RESIDUE BME N 3
18
BC9
SOFTWARE
TYR N:408 , HIS N:460 , TYR N:462 , DHB N:540
BINDING SITE FOR RESIDUE FE N 600
19
CC1
SOFTWARE
PRO B:15 , TYR B:16 , HOH B:249 , HOH N:2 , TYR N:408 , TRP N:449 , ARG N:457 , HIS N:460 , TYR N:462 , FE N:600 , HOH N:836
BINDING SITE FOR RESIDUE DHB N 540
20
CC2
SOFTWARE
ARG O:414 , ARG O:450
BINDING SITE FOR RESIDUE SO4 O 4
21
CC3
SOFTWARE
ARG O:409
BINDING SITE FOR RESIDUE CL O 1
22
CC4
SOFTWARE
TYR O:408 , HIS O:460 , TYR O:462 , DHB O:539
BINDING SITE FOR RESIDUE FE O 600
23
CC5
SOFTWARE
PRO C:15 , TYR C:16 , HOH O:3 , TYR O:408 , HIS O:447 , TRP O:449 , ARG O:457 , HIS O:460 , TYR O:462 , ILE O:491 , FE O:600 , HOH O:845
BINDING SITE FOR RESIDUE DHB O 539
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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Sorry, no Info available
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PROSITE Patterns/Profiles
(1, 6)
Info
All PROSITE Patterns/Profiles
1: INTRADIOL_DIOXYGENAS (A:51-79,B:51-79,C:51-79,M:380-408,...)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
INTRADIOL_DIOXYGENAS
PS00083
Intradiol ring-cleavage dioxygenases signature.
PCXA_PSEPU
52-80
3
A:51-79
B:51-79
C:51-79
PCXB_PSEPU
81-109
3
M:380-408
N:380-408
O:380-408
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(2, 6)
Info
All SCOP Domains
1a: SCOP_d3mv6a_ (A:)
1b: SCOP_d3mv6b_ (B:)
1c: SCOP_d3mv6c_ (C:)
2a: SCOP_d3mv6m_ (M:)
2b: SCOP_d3mv6n_ (N:)
2c: SCOP_d3mv6o_ (O:)
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Protein Domains
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)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Prealbumin-like
(433)
Superfamily
:
Aromatic compound dioxygenase
(111)
Family
:
Aromatic compound dioxygenase
(100)
Protein domain
:
Protocatechuate-3,4-dioxygenase, alpha chain
(37)
Pseudomonas putida [TaxId: 303]
(31)
1a
d3mv6a_
A:
1b
d3mv6b_
B:
1c
d3mv6c_
C:
Protein domain
:
Protocatechuate-3,4-dioxygenase, beta chain
(44)
Pseudomonas putida [TaxId: 303]
(31)
2a
d3mv6m_
M:
2b
d3mv6n_
N:
2c
d3mv6o_
O:
[
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CATH Domains
(0, 0)
Info
all CATH domains
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Pfam Domains
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Chain M
Chain N
Chain O
Asymmetric Unit 1
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select residue range 5 to 10 in all chains
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select residue range 5 to 10 in chain 'A'
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Asym.Unit (237 KB)
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